SEQanswers

Go Back   SEQanswers > Search Forums

Showing results 1 to 9 of 9
Search took 0.00 seconds.
Search: Posts Made By: thedavid
Forum: Bioinformatics 09-07-2012, 10:43 AM
Replies: 5
Views: 2,591
Posted By thedavid
Well. LifeScope is a real PITA to install. We...

Well. LifeScope is a real PITA to install. We have a nice SGE-based cluster here and support staff to install software for us. Unfortunately LifeScope appears to need it's own computer to run a...
Forum: Bioinformatics 08-28-2012, 07:22 AM
Replies: 5
Views: 2,591
Posted By thedavid
Thank mbblack. It looks like it's best to use...

Thank mbblack. It looks like it's best to use ABI's mapper.

So, what's a recommended tool to convert from colorspace to basespace after mapping? I can't figure out if ABI provides one.
Forum: Bioinformatics 08-27-2012, 12:28 PM
Replies: 5
Views: 2,591
Posted By thedavid
Recommendations for RNA-seq mapping for ABI/Illumina data-sets

I'm trying to compare transcriptomes of developing zebrafish and have tracked down RNA-seq data-sets for several of the time-points I'm interested in.

The problem is that there are three different...
Forum: Bioinformatics 07-26-2012, 01:25 PM
Replies: 16
Views: 3,203
Posted By thedavid
Sorry, first let me start off by saying it's...

Sorry, first let me start off by saying it's possible I've totally mis-understood your issue.
Second, if you fail to deal with the strand of your features (ie is the gene on the positive or negative...
Forum: Bioinformatics 07-26-2012, 01:12 PM
Replies: 16
Views: 3,203
Posted By thedavid
Is it a strand issue? I've made that mistake...

Is it a strand issue? I've made that mistake before......
Forum: Bioinformatics 07-26-2012, 01:11 PM
Replies: 2
Views: 5,452
Posted By thedavid
Get peaks from your bed files (macs14 or...

Get peaks from your bed files (macs14 or macs2)......intersectBed (to find the overlapping peaks)....output to a text file.....import into R.....run your correlation coefficient on the scores (from...
Forum: Bioinformatics 07-20-2012, 08:05 AM
Replies: 4
Views: 4,721
Posted By thedavid
UCSC genome browser -> genome of choice (hg18 or...

UCSC genome browser -> genome of choice (hg18 or hg19) -> Tables -> Groups(Genes...) -> Track (RefSeq)

When you output you have the option of selecting the format (bed) and can pick whether you...
Forum: Literature Watch 04-09-2012, 07:45 AM
Replies: 19
Views: 17,596
Posted By thedavid
1. Thanks, I'll give it a try. 2. Sorry, I...

1. Thanks, I'll give it a try.
2. Sorry, I wasn't clear - if the Klenow was added, then 10 mM dNTPs were added. What I meant was that 100 uM dNTPs were added instead of 100 uM T-mix. As a control,...
Forum: Literature Watch 04-06-2012, 11:45 AM
Replies: 19
Views: 17,596
Posted By thedavid
Has anyone not in Hinrich Gronemeyer's lab gotten...

Has anyone not in Hinrich Gronemeyer's lab gotten this process to work? I've been trying for well over a month to get it working. After a tremendous amount of troubleshooting I've made a few...
Showing results 1 to 9 of 9

 

All times are GMT -8. The time now is 06:39 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO